def main():
# getting the tree
tree_gen = Phylo.parse(PATH_EXAMPLE, 'newick')
tree_object = next(tree_gen)
# the tree basic information
print(tree_info(tree_object))
# drawing the tree
Phylo.draw(tree_object)
# distance comparing
tns = dendropy.TaxonNamespace()
tre_one = Tree.get_from_path(PATH_EXAMPLE, 'newick', taxon_namespace=tns)
tre_two = Tree.get_from_path(PATH_BIF, 'newick', taxon_namespace=tns)
euclidean_distance = treecompare.euclidean_distance(tre_one, tre_two)
robinson_distance = treecompare.robinson_foulds_distance(tre_one, tre_two)
print("Robinson Foulds distance: ", robinson_distance)
print("Euclidean distance: ", euclidean_distance)
# common ancestors
common_ancestor_tree = tree_object.common_ancestor({"name": "C"},
{"name": "D"})
common_ancestor_tree.color = "blue"
print("COMMON ANCESTOR: ", common_ancestor_tree)
Phylo.draw(common_ancestor_tree)
def calcDistance(self):
if self.path1 != '' and self.path2 != '':
self.fileEx1 = (os.path.splitext(self.path1)[1])[1:]
self.fileEx2 = (os.path.splitext(self.path2)[1])[1:]
tns = dendropy.TaxonNamespace()
self.tree1 = dendropy.Tree.get_from_path(self.path1, self.fileEx1, taxon_namespace=tns)
self.tree2 = dendropy.Tree.get_from_path(self.path2, self.fileEx2, taxon_namespace=tns)
self.tree1.encode_bipartitions()
self.tree2.encode_bipartitions()
print(treecompare.false_positives_and_negatives(self.tree1, self.tree2))
# self.tree1 = dendropy.Tree.get_from_string('((A, B), (C, D))', 'newick')
# self.tree2 = dendropy.Tree.get_from_string('((A, B), (C, D))', 'newick')
# self.tree1.encode_bipartitions()
# self.tree2.encode_bipartitions()
# oblicz dystans
# self.symDist = self.tree1.symmetric_difference(self.tree2)
self.symDist = treecompare.symmetric_difference(self.tree1, self.tree2)
self.fpnDist = treecompare.false_positives_and_negatives(self.tree1, self.tree2)
self.eucDist = treecompare.euclidean_distance(self.tree1, self.tree2)
self.rfDist = treecompare.robinson_foulds_distance(self.tree1, self.tree2)
# pokaz wyniki
self.res1.setText(str(self.eucDist)) #eucDist
self.res2.setText(str(self.rfDist)) #rfDist
def distance(file_path, file_format, file_path2):
taxon_namespace = dendropy.TaxonNamespace()
tree1 = dendropy.Tree.get_from_path(file_path,
file_format,
taxon_namespace=taxon_namespace)
tree2 = dendropy.Tree.get_from_path(file_path2,
file_format,
taxon_namespace=taxon_namespace)
sym_diff = treecompare.symmetric_difference(tree1, tree2)
euc_dis = treecompare.euclidean_distance(tree1, tree2)
false_pos = treecompare.false_positives_and_negatives(tree1, tree2)
robinson_dis = treecompare.robinson_foulds_distance(tree1, tree2)
print("Symetric difference: ", sym_diff)
print("Robinson Foulds distance: ", robinson_dis)
print("False positives and negatives: ", false_pos)
print("Euclidean distance: ", euc_dis)
def calcDistance(self):
if self.path1 != '' and self.path2 != '':
self.fileEx1 = (os.path.splitext(self.path1)[1])[1:]
self.fileEx2 = (os.path.splitext(self.path2)[1])[1:]
tns = dendropy.TaxonNamespace()
self.tree1 = dendropy.Tree.get_from_path(self.path1,
self.fileEx1,
taxon_namespace=tns)
self.tree2 = dendropy.Tree.get_from_path(self.path2,
self.fileEx2,
taxon_namespace=tns)
self.tree1.encode_bipartitions()
self.tree2.encode_bipartitions()
print(
treecompare.false_positives_and_negatives(
self.tree1, self.tree2))
# self.tree1 = dendropy.Tree.get_from_string('((A, B), (C, D))', 'newick')
# self.tree2 = dendropy.Tree.get_from_string('((A, B), (C, D))', 'newick')
# self.tree1.encode_bipartitions()
# self.tree2.encode_bipartitions()
# oblicz dystans
# self.symDist = self.tree1.symmetric_difference(self.tree2)
self.symDist = treecompare.symmetric_difference(
self.tree1, self.tree2)
self.fpnDist = treecompare.false_positives_and_negatives(
self.tree1, self.tree2)
self.eucDist = treecompare.euclidean_distance(
self.tree1, self.tree2)
self.rfDist = treecompare.robinson_foulds_distance(
self.tree1, self.tree2)
# pokaz wyniki
self.res1.setText(str(self.eucDist)) #eucDist
self.res2.setText(str(self.rfDist)) #rfDist
def calculateDistance(self):
if self.path1 != '' and self.path2 != '':
#get files extensions
self.fileExtension1 = (os.path.splitext(self.path1)[1])[1:]
self.fileExtension2 = (os.path.splitext(self.path2)[1])[1:]
#open tree files
tns = dendropy.TaxonNamespace()
self.tree1 = dendropy.Tree.get_from_path(self.path1, self.fileExtension1, taxon_namespace=tns)
self.tree2 = dendropy.Tree.get_from_path(self.path2, self.fileExtension2, taxon_namespace=tns)
self.tree1.encode_bipartitions()
self.tree2.encode_bipartitions()
print(treecompare.false_positives_and_negatives(self.tree1, self.tree2))
# self.tree1 = dendropy.Tree.get_from_string('((A, B), (C, D))', 'newick')
# self.tree2 = dendropy.Tree.get_from_string('((A, B), (C, D))', 'newick')
# self.tree1.encode_bipartitions()
#self.tree2.encode_bipartitions()
#calculate distances
#self.symDist = self.tree1.symmetric_difference(self.tree2)
self.symDist = treecompare.symmetric_difference(self.tree1, self.tree2)
self.fpnDist = treecompare.false_positives_and_negatives(self.tree1, self.tree2)
self.eucDist = treecompare.euclidean_distance(self.tree1, self.tree2)
self.rfDist = treecompare.robinson_foulds_distance(self.tree1, self.tree2)
#show distances
self.dist1Value.setText(str(self.eucDist))
self.dist2Value.setText(str(self.rfDist))
self.dist3Value.setText(str(self.symDist))
self.dist4Value.setText(str(self.fpnDist))
import sys
import dendropy
from dendropy.calculate import treecompare
t1_filename = sys.argv[1]
t2_filename = sys.argv[2]
# Create taxon namespace
tns = dendropy.TaxonNamespace()
# Read in the trees
t1 = dendropy.Tree.get(path=t1_filename, schema="newick", taxon_namespace=tns)
t2 = dendropy.Tree.get(path=t2_filename, schema="newick", taxon_namespace=tns)
# Calculate rf distance
rf_dist = treecompare.robinson_foulds_distance(t1, t2)
# Calculate weighted rf distance
weighted_rf_dist = treecompare.weighted_robinson_foulds_distance(t1, t2)
print("Your rf dist: " + str(rf_dist) + ".")
print("Your weighted rf dist: " + str(weighted_rf_dist) + ".")
import dendropy
from dendropy.calculate import treecompare
trees = dendropy.TreeList.get(path="pythonidae.random.bd0301.tre",
schema="nexus")
for tree in trees:
print(tree.as_string("newick"))
print(len(trees))
print(trees[4].as_string("nexus"))
print(treecompare.robinson_foulds_distance(trees[0], trees[1]))
print(treecompare.weighted_robinson_foulds_distance(trees[0], trees[1]))
first_10_trees = trees[:10]
last_10_trees = trees[-10:]
# Note that the TaxonNamespace is propogated to slices
assert first_10_trees.taxon_namespace is trees.taxon_namespace
assert first_10_trees.taxon_namespace is trees.taxon_namespace
print(id(trees[4]))
print(id(trees[5]))
trees[4] = trees[5]
print(id(trees[4]))
print(id(trees[5]))
print(trees[4] in trees)
trees.remove(trees[-1])
tx = trees.pop()
import dendropy
from dendropy.calculate import treecompare
trees = dendropy.TreeList.get(
path="pythonidae.random.bd0301.tre",
schema="nexus")
for tree in trees:
print(tree.as_string("newick"))
print(len(trees))
print(trees[4].as_string("nexus"))
print(treecompare.robinson_foulds_distance(trees[0], trees[1]))
print(treecompare.weighted_robinson_foulds_distance(trees[0], trees[1]))
first_10_trees = trees[:10]
last_10_trees = trees[-10:]
# Note that the TaxonNamespace is propogated to slices
assert first_10_trees.taxon_namespace is trees.taxon_namespace
assert first_10_trees.taxon_namespace is trees.taxon_namespace
print(id(trees[4]))
print(id(trees[5]))
trees[4] = trees[5]
print(id(trees[4]))
print(id(trees[5]))
print(trees[4] in trees)
